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Arya M, Ghosh A, Tyagi K, Tyagi I, Bisht SS, Kumar V. Characterization of Complete Mitochondrial Genome of Badri Breed of Bos indicus (Bovidae: Bovinae): Selection Pressure and Comparative Analysis. Biochem Genet 2025; 63:43-66. [PMID: 38407767 DOI: 10.1007/s10528-024-10691-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/05/2024] [Indexed: 02/27/2024]
Abstract
High-altitude mammals are often subject to specific environmental obstacles, which exert selective pressure on their physiological and morphological traits, hence driving their evolutionary processes. It is anticipated that these circumstances will lead to the adaptive evolution of protein-coding genes (PCGs) in the mitochondrial genome, which play a crucial role in the oxidative phosphorylation system. In this study, we have generated the complete mitochondrial genome of the Badri breed of Bos indicus inhabiting a high-altitude environment to test the signatures of adaptive evolution on PCGs and their phylogenetic relationships. The complete mitogenome of the Badri breed is 16,339 bp and most tRNAs showed typical clover-leaf secondary structure with a few exceptions, like trnS1 and trnS2 without DHU arm and trnK without DHU loop. Comparative analysis of PCGs indicated that cox1 is the most conserved, while atp6 is the most variable gene. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated the purifying selection (Ka/Ks < 1) in the protein-coding genes that shape the diversity in mitogenome of Bos indicus. Furthermore, Branch-site model (BSM) suggested that cox1, cox2, nad3, nad4L, and nad6 underwent stronger purifying selection (ω < 1) than other PCGs in 15 breeds of 4 species, including Badri. BSM also detected 10 positive sites in PCGs and one in 13 PCGs concatenated dataset. Additional analyses in Datamonkey indicated 11 positive sites and 23 purifying sites in the concatenated dataset, a relaxation of selection strength in nad3, and no evidence of episodic diversifying selection in any PCGs. Phylogeny revealed the sister relationship of the Badri with other breeds of Bos indicus as well as Bos frontalis (Gayal-2). The mitogenome of the Badri breed is an important genomic resource for conservation genetics of this species and also contributes to the understanding of the adaptive evolution of mitochondrial protein coding genes.
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Affiliation(s)
- Mansi Arya
- Department of Zoology, Kumaun University, Nainital, Uttarakhand, India
| | - Abhishek Ghosh
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Satpal Singh Bisht
- Department of Zoology, Kumaun University, Nainital, Uttarakhand, India
- Vice Chancellor, Soban Singh Jeena University, Almora, Uttarakahand, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
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Ghosh A, Tyagi K, Banerjee D, Kumar V. Mitogenomics providing new insights into the phylogenetic structure of subfamily Panchaetothripinae (Thripidae: Terebrantia). Genetica 2024; 153:3. [PMID: 39585444 DOI: 10.1007/s10709-024-00218-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 10/31/2024] [Indexed: 11/26/2024]
Abstract
Complete mitochondrial genome of two species of subfamily Panchaetothripinae, Astrothrips tumiceps (16,467 bp) and Monilothrips kempi (14,773 bp) are generated by Next-Generation Sequencing Method. In this study, the detailed annotation of these mitogenomes as well as comparative analyses are carried out to explore the codon usage, gene composition, and phylogenetic relationship of subfamilies of family Thripidae. Moreover, the gene rearrangement of subfamily Panchaetothripinae of family Thripidae is also studied. Both the mitogenomes featured by 37 genes including 13 PCGs, 22 tRNAs, 2 rRNAs and with single putative control region with a positive AT-skew and negative GC-skew. trnS1 without DHU arm in both species, trnV without DHU arm in M. kempi, and trnE without TΨC loop in As. tumiceps. Further, codon based comparative analysis depicted the existence of natural selection pressure on all the PCGs in all the subfamilies of family Thripidae. The phylogenetic analyses, using the Bayesian inference (BI) and Maximum likelihood (ML) supported the monophyly of two suborders and family Phlaeothripidae. The family Thripidae is recovered as paraphyletic and subfamily Panchaetothripinae is in sister relationship with family Aeolothripidae and Stenurothripidae rather than the other subfamilies of family Thripidae. The gene order of the order Thysanoptera is highly rearranged, while few members of the subfamily Panchaetothripinae showed similar gene order to family Stenurothripidae. Therefore, this study suggests that the phylogenetic relationship between the subfamily Panchaetothripinae and other families is uncertain, necessitating a whole genome-based study to clarify the position of Panchaetothripinae within the suborder Terebrantia.
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Affiliation(s)
- Abhishek Ghosh
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Dhriti Banerjee
- Director Lab, Zoological Survey of India, Kolkata, West Bengal, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
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Li J, Wu H, Zhou Y, Liu M, Zhou Y, Chu J, Kamili E, Wang W, Yang J, Lin L, Zhang Q, Yang S, Xu Y. Characterization and trans-generation dynamics of mitogene pool in the silver carp (Hypophthalmichthys molitrix). G3 (BETHESDA, MD.) 2024; 14:jkae101. [PMID: 38922124 PMCID: PMC11491513 DOI: 10.1093/g3journal/jkae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 06/27/2024]
Abstract
Multicopied mitogenome are prone to mutation during replication often resulting in heteroplasmy. The derived variants in a cell, organ, or an individual animal constitute a mitogene pool. The individual mitogene pool is initiated by a small fraction of the egg mitogene pool. However, the characteristics and relationship between them has not yet been investigated. This study quantitatively analyzed the heteroplasmy landscape, genetic loads, and selection strength of the mitogene pool of egg and hatchling in the silver carp (Hypophthalmichthys molitrix) using high-throughput resequencing. The results showed heteroplasmic sites distribute across the whole mitogenome in both eggs and hatchlings. The dominant substitution was Transversion in eggs and Transition in hatching accounting for 95.23%±2.07% and 85.38%±6.94% of total HP sites, respectively. The total genetic loads were 0.293±0.044 in eggs and 0.228±0.022 in hatchlings (P=0.048). The dN/dS ratio was 58.03±38.98 for eggs and 9.44±3.93 for hatchlings (P=0.037). These results suggest that the mitogenomes were under strong positive selection in eggs with tolerance to variants with deleterious effects, while the selection was positive but much weaker in hatchlings showing marked quality control. Based on these findings, we proposed a trans-generation dynamics model to explain differential development mode of the two mitogene pool between oocyte maturation and ontogenesis of offspring. This study sheds light on significance of mitogene pool for persistence of populations and subsequent integration in ecological studies and conservation practices.
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Affiliation(s)
- Jinlin Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Hengshu Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Yingna Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Manhong Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Yongheng Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Jianing Chu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Elizabeth Kamili
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Wenhui Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Jincheng Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Lijun Lin
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Qi Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
| | - Shuhui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin 150040, China
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Yang YX, Kang Y, Ge XY, Yuan SL, Li XY, Liu HY. A Mysterious Asian Firefly Genus, Oculogryphus Jeng, Engel & Yang (Coleoptera, Lampyridae): The First Complete Mitochondrial Genome and Its Phylogenetic Implications. INSECTS 2024; 15:464. [PMID: 39057197 PMCID: PMC11277304 DOI: 10.3390/insects15070464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024]
Abstract
The firefly genus Oculogryphus Jeng, Engel & Yang, 2007 is a rare-species group endemic to Asia. Since its establishment, its position has been controversial but never rigorously tested. To address this perplexing issue, we are the first to present the complete mitochondrial sequence of Oculogryphus, using the material of O. chenghoiyanae Yiu & Jeng, 2018 determined through a comprehensive morphological identification. Our analyses demonstrate that its mitogenome exhibits similar characteristics to that of Stenocladius, including a rearranged gene order between trnC and trnW, and a long intergenic spacer (702 bp) between the two rearranged genes, within which six remnants (29 bp) of trnW were identified. Further, we incorporated this sequence into phylogenetic analyses of Lampyridae based on different molecular markers and datasets using ML and BI analyses. The results consistently place Oculogryphus within the same clade as Stenocladius in all topologies, and the gene rearrangement is a synapomorphy for this clade. It suggests that Oculogryphus should be classified together with Stenocladius in the subfamily Ototretinae at the moment. This study provides molecular evidence confirming the close relationship between Oculogryphus and Stenocladius and discovers a new phylogenetic marker helpful in clarifying the monophyly of Ototretinae, which also sheds a new light on firefly evolution.
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Affiliation(s)
- Yu-Xia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China
| | - Ya Kang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Xue-Ying Ge
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Shuai-Long Yuan
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hao-Yu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; (Y.-X.Y.); (Y.K.); (X.-Y.G.); (S.-L.Y.)
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China
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Lee Y, Kim KB, Choi EH, Hwang UW. Complete mitochondrial genome of the worm snail Thylacodes adamsii (Littorinimorpha: Vermetidae) from South Korea. Mitochondrial DNA B Resour 2024; 9:753-757. [PMID: 38895513 PMCID: PMC11185085 DOI: 10.1080/23802359.2024.2368209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
The worm snail Thylacodes adamsii (Mörch, 1859) (Littorinimorpha: Vermetidae) is a sessile gastropod that mainly inhabits rocky shores along the warm temperate to tropical ocean. Herein, the complete mitochondrial genome (mitogenome) of T. adamsii from South Korea was characterized. The genome is 14,913 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The genome organization and base composition of T. adamsii are similar to those of other vermetids. A phylogenetic tree was reconstructed using maximum likelihood based on the nucleotide sequences of the 13 PCGs; this tree supported the monophyly of Vermetidae. The complete mitogenome of T. adamsii can assist with molecular species identification and vermetid phylogenetic research in the future.
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Affiliation(s)
- Yumin Lee
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Ki Beom Kim
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
| | - Eun Hwa Choi
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Phylomics Inc., Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
- Phylomics Inc., Daegu, South Korea
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
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Xu X, Huang H, Lin S, Zhou L, Yi Y, Lin E, Feng L, Zheng Y, Lin A, Yu L, Shen Y, Henry RJ, Fang J. Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species. BMC PLANT BIOLOGY 2024; 24:331. [PMID: 38664619 PMCID: PMC11044428 DOI: 10.1186/s12870-024-04995-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Jasmine (Jasminum), renowned for its ornamental value and captivating fragrance, has given rise to numerous species and accessions. However, limited knowledge exists regarding the evolutionary relationships among various Jasminum species. RESULTS In the present study, we sequenced seven distinct Jasminum species, resulting in the assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that the size of the 12 cp genomes ranged from 159 to 165 kb and encoded 134-135 genes, including 86-88 protein-coding genes, 38-40 tRNA genes, and 8 rRNA genes. J. nudiflorum exhibited a larger genome size compared to other species, mainly attributed to the elevated number of forward repeats (FRs). Despite the typically conservative nature of chloroplasts, variations in the presence or absence of accD have been observed within J. sambac. The calculation of nucleotide diversity (Pi) values for 19 cp genomes indicated that potential mutation hotspots were more likely to be located in LSC regions than in other regions, particularly in genes ycf2, rbcL, atpE, ndhK, and ndhC (Pi > 0.2). Ka/Ks values revealed strong selection pressure on the genes rps2, atpA, rpoA, rpoC1, and rpl33 when comparing J. sambac with the three most closely related species (J. auriculatum, J. multiflorum, and J. dichotomum). Additionally, SNP identification, along with the results of Structure, PCA, and phylogenetic tree analyses, divided the Jasminum cp genomes into six groups. Notably, J. polyanthum showed gene flow signals from both the G5 group (J. nudiflorum) and the G3 group (J. tortuosum and J. fluminense). Phylogenetic tree analysis reflected that most species from the same genus clustered together with robust support in Oleaceae, strongly supporting the monophyletic nature of cp genomes within the genus Jasminum. CONCLUSION Overall, this study provides comprehensive insights into the genomic composition, variation, and phylogenetic relationships among various Jasminum species. These findings enhance our understanding of the genetic diversity and evolutionary history of Jasminum.
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Affiliation(s)
- Xiuming Xu
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Hechen Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Linwei Zhou
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Yuchong Yi
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Enwen Lin
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Yu Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Aiting Lin
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
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Wang G, An J, Si J. The complete chloroplast genome sequence of Rhamnella wilsonii Schneid (Rhamnaceae). Mitochondrial DNA B Resour 2024; 9:488-492. [PMID: 38623175 PMCID: PMC11018004 DOI: 10.1080/23802359.2024.2339492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Rhamnella wilsonii Schneid 1914 is a member of the Rhamnaceae and endemic to China. In this study, the complete chloroplast genome of R. wilsonii was sequenced and assembled. The complete chloroplast genome was 160,049 bp in length, including a pair of inverted repeats (IRs) of 26,502 bp, one large single copy (LSC) region of 88,274 bp and one small single copy (SSC) region of 18,771 bp. The genome contained 129 genes, including 8 rRNA genes, 37 tRNA genes and 84 protein-coding genes. The overall GC content of the complete chloroplast genome was 37.15%. The phylogenetic analysis demonstrated that R. wilsonii is closely related to R. martinni. This study provides basic information for further studies on the identification and evolution of R. wilsonii and Rhamnella from genomic perspective.
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Affiliation(s)
- Gaini Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Jilong An
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Jianping Si
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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Kuo LY, Su HJ, Koubínová D, Xie PJ, Whitehouse C, Ebihara A, Grant JR. Organellar phylogenomics of Ophioglossaceae fern genera. FRONTIERS IN PLANT SCIENCE 2024; 14:1294716. [PMID: 38288414 PMCID: PMC10823028 DOI: 10.3389/fpls.2023.1294716] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024]
Abstract
Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.
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Affiliation(s)
- Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
| | - Darina Koubínová
- University of Neuchâtel, Laboratory of Evolutionary Genetics, Neuchâtel, Switzerland
| | - Pei-Jun Xie
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Jason R. Grant
- University of Neuchâtel, Laboratory of Evolutionary Genetics, Neuchâtel, Switzerland
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Mukherjee A, Ghosh A, Tyagi K, Kumar V, Banerjee D, Naskar A. Characterization of complete mitochondrial genome of three Horse flies of the genus Tabanus (Diptera: Tabanidae): comparative analysis. Mol Biol Rep 2023; 50:9897-9908. [PMID: 37864662 DOI: 10.1007/s11033-023-08837-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Tabanidae (Horse-Flies or Deer-Flies) are one of the most economically important as well as medically significant haematophagous insect family within the order Diptera. Members of this group are also responsible for the mortality of substantial number of live-stock every year. Due to their pathogen transmission potential and vector competencies makes them an important insect group to study. Till now, mitochondrial genome of 18 species of tabanids were available. METHODS AND RESULTS The complete mitogenome of three species T. diversifrons (15,809 bp), T. rubidus (15,878 bp) and T. tenens (15,872 bp) were generated by Next generation sequencing method. They consist 37 genes, with a positive AT skew and a negative GC skew. The gene order of these three species is similar to the typical gene arrangement of infra-order Tabanomorpha. Most of the tRNAs showed typical clover-leaf secondary structure except trnS1, which lacks the DHU arm. The sliding window analysis showed that the nad4L is the most conserved while atp8, and nad6 are the most variable genes. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated that all PCGs under the purifying selection. Phylogeny revealed Chrysops and Haematopota are monophyletic while species of Hybomitra are nested within the polyphyletic clade of Tabanus. T. diversifrons exhibits sister relationship with Atylotus miser. Two morphologically divergent species T. rubidus and T. tenens are found to be genetically similar and indistinguishable by mitochondrial genome. CONCLUSIONS The hypervariable genes like atp8 and nad6 can be used as molecular markers for the identification of recently diverged lineages of family Tabanidae. Further, to address uncertainties arising from the two morphological divergent species, it is imperative to obtain data from nuclear gene markers.
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Affiliation(s)
- Arka Mukherjee
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Abhishek Ghosh
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Dhriti Banerjee
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
| | - Atanu Naskar
- Diptera Section, Zoological Survey of India, Kolkata, West Bengal, India
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Liu K, Xie N, Wang Y, Liu X. Extensive mitogenomic heteroplasmy and its implications in the phylogeny of the fish genus Megalobrama. 3 Biotech 2023; 13:115. [PMID: 36915286 PMCID: PMC10006376 DOI: 10.1007/s13205-023-03523-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
Megalobrama is China's most economically valuable fish genera. Four species make up this genus: M. amblycephala (MA), M. terminalis (MT), M. pellegrini (MP), and M. hoffmanni (MH). Many researchers have investigated the genetic relationship of Megalobrama based on mitochondrial DNA (mtDNA) and discovered that the branches of the phylogenetic tree for MT and MP are intertwined. We hypothesized that this occurs because mitogenomic heteroplasmy is overlooked when working with mtDNA, which causes MP and MT positions to intersect in phylogenetic trees. To eliminate the influence of nuclear mitochondrial DNA fragments (NUMTs) before analyzing mitogenomic heteroplasmy, we used PLastZ to identify NUMTs, which were then removed from the samples for the subsequent heteroplasmy analysis. Using the heteroplasmy caller icHET, we discovered 126, 339, 135, and 203 heteroplasmic variants in six MA, MT, MP, and MH samples. We reconstructed the Megalobrama fish genus's phylogenetic tree using the RY coding method and rejecting the third position on codons, which improved the performance of the phylogenetic tree by increasing the ratio of treeness to relative component variability from 100.02 ± 1.76 to 688.59 ± 190.56. Despite this, the RY coding method cannot alter the intersection of MP and MT positions in phylogenetic trees. We hypothesize that gene flow between MT and MP leads to intertwining mtDNA-based phylogenetic trees. In conclusion, our findings on the mitogenomic heteroplasmy of Megalobrama provide new insights into mtDNA-based phylogenetic studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03523-0.
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Affiliation(s)
- Kai Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yuxi Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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11
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Wang P, Wang F. A proposed metric set for evaluation of genome assembly quality. Trends Genet 2023; 39:175-186. [PMID: 36402623 DOI: 10.1016/j.tig.2022.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022]
Abstract
Quality control is essential for genome assemblies; however, a consensus has yet to be reached on what metrics should be adopted for the evaluation of assembly quality. N50 is widely used for contiguity measurement, but its effectiveness is constantly in question. Prevailing metrics for the completeness evaluation focus on gene space, yet challenging areas such as tandem repeats are commonly overlooked. Achieving correctness has become an indispensable dimension for quality control, while prevailing assembly releases lack scores reflecting this aspect. We propose a metric set with a set of statistic indexes for effective, comprehensive evaluation of assemblies and provide a score of a finished assembly for each metric, which can be utilized as a benchmark for achieving high-quality genome assemblies.
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Affiliation(s)
- Peng Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture and Rural Affairs, Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, No. 4 Xueyuan Rd, Haikou City, Hainan 571101, China.
| | - Fei Wang
- School of Electrical and Electronic Engineering, Shanghai Institute of Technology, No. 100 Haiquan Rd, Shanghai 201416, China.
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12
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Multichromosomal Mitochondrial Genome of Paphiopedilum micranthum: Compact and Fragmented Genome, and Rampant Intracellular Gene Transfer. Int J Mol Sci 2023; 24:ijms24043976. [PMID: 36835385 PMCID: PMC9966765 DOI: 10.3390/ijms24043976] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Orchidaceae is one of the largest families of angiosperms. Considering the large number of species in this family and its symbiotic relationship with fungi, Orchidaceae provide an ideal model to study the evolution of plant mitogenomes. However, to date, there is only one draft mitochondrial genome of this family available. Here, we present a fully assembled and annotated sequence of the mitochondrial genome (mitogenome) of Paphiopedilum micranthum, a species with high economic and ornamental value. The mitogenome of P. micranthum was 447,368 bp in length and comprised 26 circular subgenomes ranging in size from 5973 bp to 32,281 bp. The genome encoded for 39 mitochondrial-origin, protein-coding genes; 16 tRNAs (three of plastome origin); three rRNAs; and 16 ORFs, while rpl10 and sdh3 were lost from the mitogenome. Moreover, interorganellar DNA transfer was identified in 14 of the 26 chromosomes. These plastid-derived DNA fragments represented 28.32% (46,273 bp) of the P. micranthum plastome, including 12 intact plastome origin genes. Remarkably, the mitogenome of P. micranthum and Gastrodia elata shared 18% (about 81 kb) of their mitochondrial DNA sequences. Additionally, we found a positive correlation between repeat length and recombination frequency. The mitogenome of P. micranthum had more compact and fragmented chromosomes compared to other species with multichromosomal structures. We suggest that repeat-mediated homologous recombination enables the dynamic structure of mitochondrial genomes in Orchidaceae.
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Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, Chen G, Ng WL, Islam MN, Punnarak P, Zheng H, Zhu X. A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea. FRONTIERS IN PLANT SCIENCE 2023; 13:1075353. [PMID: 36684775 PMCID: PMC9845719 DOI: 10.3389/fpls.2022.1075353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
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Affiliation(s)
- Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuchen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qianying Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Luzhen Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Md Nazrul Islam
- Forestry and Wood Technology Discipline, Khulna University, Khulna, Bangladesh
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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14
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An R, Niu M, Lou X, Huang H, Lin E. The complete chloroplast genome of Rhododendron huadingense (Ericaceae). Mitochondrial DNA B Resour 2022; 7:1910-1912. [PMCID: PMC9629095 DOI: 10.1080/23802359.2022.2135403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Ran An
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingyue Niu
- Huading Forestry Farm, Tiantai, Zhejiang, China
| | - Xiongzhen Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Huahong Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Erpei Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
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15
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Wilder AP, Dudchenko O, Curry C, Korody M, Turbek SP, Daly M, Misuraca A, Gaojianyong WANG, Khan R, Weisz D, Fronczek J, Aiden EL, Houck ML, Shier DM, Ryder OA, Steiner CC. A chromosome-length reference genome for the endangered Pacific pocket mouse reveals recent inbreeding in a historically large population. Genome Biol Evol 2022; 14:6650481. [PMID: 35894178 PMCID: PMC9348616 DOI: 10.1093/gbe/evac122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.
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Affiliation(s)
- Aryn P Wilder
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, USA
| | - Caitlin Curry
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Marisa Korody
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Sheela P Turbek
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA.,Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | | | - Ann Misuraca
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - W A N G Gaojianyong
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - Julie Fronczek
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, USA.,UWA School of Agriculture and Environment, The University of Western Australia, Australia.,Broad Institute of MIT and Harvard, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, China
| | - Marlys L Houck
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Debra M Shier
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA.,Department of Ecology & Evolutionary Biology, University of California Los Angeles, USA
| | - Oliver A Ryder
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Cynthia C Steiner
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
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16
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Zhou X, Lv Y, Zhang J, Wang D, Wang Z, Zhou Y, Wang W. The complete chloroplast genome sequence of Nymphoides peltata (S.G.Gmel.) Kuntze. Mitochondrial DNA B Resour 2022; 7:1406-1407. [PMID: 35923642 PMCID: PMC9341379 DOI: 10.1080/23802359.2022.2098851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nymphoides peltata is an aquatic floating weed widely distributed in the northern hemisphere of Eurasia. To better determine its phylogenetic relationships with other Nymphoides species and other aquatic plant species, the chloroplast genome of N. peltata was sequenced. The chloroplast genome size is 152,198 bp, consisting of a large single-copy region (84,223 bp) and a small single-copy region (17,817 bp) separated by a pair of inverted repeats with a length of 25,079 bp. The chloroplast genome contains 127 genes, including 85 protein-coding genes, 34 tRNA genes, and eight rRNAs. The maximum-likelihood phylogenetic tree showed that N. peltata is more closely related to other Nymphoides species, providing new insight into the evolution and genetic diversity of aquatic weeds.
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Affiliation(s)
- Xiangqin Zhou
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Hainan University, Haikou, People’s Republic of China
| | - Yudie Lv
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Hainan University, Haikou, People’s Republic of China
| | - Jingtao Zhang
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Hainan University, Haikou, People’s Republic of China
| | - Dongling Wang
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Hainan University, Haikou, People’s Republic of China
| | - Zihao Wang
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Hainan University, Haikou, People’s Republic of China
| | - Yuan Zhou
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Hainan University, Haikou, People’s Republic of China
| | - Wenfeng Wang
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Hainan University, Haikou, People’s Republic of China
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17
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Degradi L, Tava V, Prigitano A, Esposto MC, Tortorano AM, Saracchi M, Kunova A, Cortesi P, Pasquali M. Exploring Mitogenomes Diversity of Fusarium musae from Banana Fruits and Human Patients. Microorganisms 2022; 10:1115. [PMID: 35744633 PMCID: PMC9227538 DOI: 10.3390/microorganisms10061115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/10/2022] Open
Abstract
Fusarium musae has recently been described as a cross-kingdom pathogen causing post-harvest disease in bananas and systemic and superficial infection in humans. The taxonomic identity of fungal cross-kingdom pathogens is essential for confirming the identification of the species on distant infected hosts. Understanding the level of variability within the species is essential to decipher the population homogeneity infecting human and plant hosts. In order to verify that F. musae strains isolated from fruits and patients are part of a common population and to estimate their overall diversity, we assembled, annotated and explored the diversity of the mitogenomes of 18 F. musae strains obtained from banana fruits and human patients. The mitogenomes showed a high level of similarity among strains with different hosts' origins, with sizes ranging from 56,493 to 59,256 bp. All contained 27 tRNA genes and 14 protein-coding genes, rps3 protein, and small and large ribosomal subunits (rns and rnl). Variations in the number of endonucleases were detected. A comparison of mitochondrial endonucleases distribution with a diverse set of Fusarium mitogenomes allowed us to specifically discriminate F. musae from its sister species F. verticillioides and the other Fusarium species. Despite the diversity in F. musae mitochondria, strains from bananas and strains from human patients group together, indirectly confirming F. musae as a cross-kingdom pathogen.
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Affiliation(s)
- Luca Degradi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Valeria Tava
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Anna Prigitano
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Maria Carmela Esposto
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Anna Maria Tortorano
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Marco Saracchi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Andrea Kunova
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Paolo Cortesi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
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18
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Lüth T, Schaake S, Grünewald A, May P, Trinh J, Weissensteiner H. Benchmarking Low-Frequency Variant Calling With Long-Read Data on Mitochondrial DNA. Front Genet 2022; 13:887644. [PMID: 35664331 PMCID: PMC9161029 DOI: 10.3389/fgene.2022.887644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Sequencing quality has improved over the last decade for long-reads, allowing for more accurate detection of somatic low-frequency variants. In this study, we used mixtures of mitochondrial samples with different haplogroups (i.e., a specific set of mitochondrial variants) to investigate the applicability of nanopore sequencing for low-frequency single nucleotide variant detection. Methods: We investigated the impact of base-calling, alignment/mapping, quality control steps, and variant calling by comparing the results to a previously derived short-read gold standard generated on the Illumina NextSeq. For nanopore sequencing, six mixtures of four different haplotypes were prepared, allowing us to reliably check for expected variants at the predefined 5%, 2%, and 1% mixture levels. We used two different versions of Guppy for base-calling, two aligners (i.e., Minimap2 and Ngmlr), and three variant callers (i.e., Mutserve2, Freebayes, and Nanopanel2) to compare low-frequency variants. We used F1 score measurements to assess the performance of variant calling. Results: We observed a mean read length of 11 kb and a mean overall read quality of 15. Ngmlr showed not only higher F1 scores but also higher allele frequencies (AF) of false-positive calls across the mixtures (mean F1 score = 0.83; false-positive allele frequencies < 0.17) compared to Minimap2 (mean F1 score = 0.82; false-positive AF < 0.06). Mutserve2 had the highest F1 scores (5% level: F1 score >0.99, 2% level: F1 score >0.54, and 1% level: F1 score >0.70) across all callers and mixture levels. Conclusion: We here present the benchmarking for low-frequency variant calling with nanopore sequencing by identifying current limitations.
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Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- *Correspondence: Joanne Trinh, ; Hansi Weissensteiner,
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- *Correspondence: Joanne Trinh, ; Hansi Weissensteiner,
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19
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Nunes Godeiro N, Palacios-Vargas JG, Gao Y, Bu Y. Complete mitochondrial genome of the Mexican marine littoral hygrophilous Spinactaletes boneti (Collembola: Actaletidae) and its phylogenetic placement. Mitochondrial DNA B Resour 2022; 7:755-757. [PMID: 35528253 PMCID: PMC9067984 DOI: 10.1080/23802359.2022.2068982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
| | - José G. Palacios-Vargas
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, México
| | - Yan Gao
- Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai, China
| | - Yun Bu
- Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai, China
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20
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Bu Y, Gao Y, Nunes Godeiro N. The first complete mitochondrial genome of the micro-whip-scorpion Schizomus zhensis (Arachnida: Schizomida) and phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:709-711. [PMID: 35493713 PMCID: PMC9045771 DOI: 10.1080/23802359.2022.2067499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The first complete mitochondrial genome of the micro-whip-scorpion (Schizomus zhensis) was assembled from Illumina-based whole genome sequencing. The circular genome is 14,309 bp in length with 13 protein coding genes, 22 tRNA, 2 rRNAs, and a control region. The A + T content of the mitogenome is 76.6%. Maximum likelihood phylogenetic analyses placed Schizomus zhensis as a sister group of (Thelyphonida + Amblypygi), but more mitogenomes of Tetrapulmonata need to be included in further analyses for a conclusive decision about the group systematics.
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Affiliation(s)
- Yun Bu
- Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai, China
| | - Yan Gao
- Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai, China
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21
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Ip EKK, Troup M, Xu C, Winlaw DS, Dunwoodie SL, Giannoulatou E. Benchmarking the Effectiveness and Accuracy of Multiple Mitochondrial DNA Variant Callers: Practical Implications for Clinical Application. Front Genet 2022; 13:692257. [PMID: 35350246 PMCID: PMC8957813 DOI: 10.3389/fgene.2022.692257] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/27/2022] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations contribute to human disease across a range of severity, from rare, highly penetrant mutations causal for monogenic disorders to mutations with milder contributions to phenotypes. mtDNA variation can exist in all copies of mtDNA or in a percentage of mtDNA copies and can be detected with levels as low as 1%. The large number of copies of mtDNA and the possibility of multiple alternative alleles at the same DNA nucleotide position make the task of identifying allelic variation in mtDNA very challenging. In recent years, specialized variant calling algorithms have been developed that are tailored to identify mtDNA variation from whole-genome sequencing (WGS) data. However, very few studies have systematically evaluated and compared these methods for the detection of both homoplasmy and heteroplasmy. A publicly available synthetic gold standard dataset was used to assess four mtDNA variant callers (Mutserve, mitoCaller, MitoSeek, and MToolBox), and the commonly used Genome Analysis Toolkit “best practices” pipeline, which is included in most current WGS pipelines. We also used WGS data from 126 trios and calculated the percentage of maternally inherited variants as a metric of calling accuracy, especially for homoplasmic variants. We additionally compared multiple pathogenicity prediction resources for mtDNA variants. Although the accuracy of homoplasmic variant detection was high for the majority of the callers with high concordance across callers, we found a very low concordance rate between mtDNA variant callers for heteroplasmic variants ranging from 2.8% to 3.6%, for heteroplasmy thresholds of 5% and 1%. Overall, Mutserve showed the best performance using the synthetic benchmark dataset. The analysis of mtDNA pathogenicity resources also showed low concordance in prediction results. We have shown that while homoplasmic variant calling is consistent between callers, there remains a significant discrepancy in heteroplasmic variant calling. We found that resources like population frequency databases and pathogenicity predictors are now available for variant annotation but still need refinement and improvement. With its peculiarities, the mitochondria require special considerations, and we advocate that caution needs to be taken when analyzing mtDNA data from WGS data.
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Affiliation(s)
- Eddie K K Ip
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
| | - Michael Troup
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Colin Xu
- School of Computer Science and Engineering, Sydney, NSW, Australia
| | - David S Winlaw
- Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Centre, Heart Institute, Cincinnati, OH, United States
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, Sydney, NSW, Australia
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22
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Malkócs T, Viricel A, Becquet V, Evin L, Dubillot E, Pante E. Complex mitogenomic rearrangements within the Pectinidae (Mollusca: Bivalvia). BMC Ecol Evol 2022; 22:29. [PMID: 35272625 PMCID: PMC8915466 DOI: 10.1186/s12862-022-01976-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/18/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Scallops (Bivalvia: Pectinidae) present extraordinary variance in both mitochondrial genome size, structure and content, even when compared to the extreme diversity documented within Mollusca and Bivalvia. In pectinids, mitogenome rearrangements involve protein coding and rRNA genes along with tRNAs, and different genome organization patterns can be observed even at the level of Tribes. Existing pectinid phylogenies fail to resolve some relationships in the family, Chlamydinae being an especially problematic group. RESULTS In our study, we sequenced, annotated and characterized the mitochondrial genome of a member of Chlamydinae, Mimachlamys varia-a species of commercial interest and an effective bioindicator-revealing yet another novel gene arrangement in the Pectinidae. The phylogeny based on all mitochondrial protein coding and rRNA genes suggests the paraphyly of the Mimachlamys genus, further commending the taxonomic revision of the classification within the Chlamydinae subfamily. At the scale of the Pectinidae, we found that 15 sequence blocks are involved in mitogenome rearrangements, which behave as separate units. CONCLUSIONS Our study reveals incongruities between phylogenies based on mitochondrial protein-coding versus rRNA genes within the Pectinidae, suggesting that locus sampling affects phylogenetic inference at the scale of the family. We also conclude that the available taxon sampling does not allow for understanding of the mechanisms responsible for the high variability of mitogenome architecture observed in the Pectinidae, and that unraveling these processes will require denser taxon sampling.
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Affiliation(s)
- Tamás Malkócs
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France. .,Pál Juhász-Nagy Doctoral School of Biology and Environmental Sciences, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary. .,Institute of Biology and Ecology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary. .,Institute of Aquatic Ecology, Centre for Ecological Research, 4026, Debrecen, Hungary.
| | - Amélia Viricel
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Vanessa Becquet
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Louise Evin
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Emmanuel Dubillot
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Eric Pante
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
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23
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Degradi L, Tava V, Kunova A, Cortesi P, Saracchi M, Pasquali M. Telomere to Telomere Genome Assembly of Fusarium musae F31, Causal Agent of Crown Rot Disease of Banana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1455-1457. [PMID: 34388352 DOI: 10.1094/mpmi-05-21-0127-a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fusarium musae causes crown rot of banana and it is also associated to clinical fusariosis. A chromosome-level genome assembly of F. musae F31 obtained combining Nanopore long reads and Illumina paired-end reads resulted in 12 chromosomes plus one contig with overall N50 of 4.36 Mb, and is presented together with its mitochondrial genome (58,072 bp). The F31 genome includes telomeric regions for 11 of the 12 chromosomes representing one of the most complete genomes available in the Fusarium fujikuroi species complex. The high-quality assembly of the F31 genome will be a valuable resource for studying the pathogenic interactions occurring between F. musae and banana. Moreover, it represents an important resource for understanding the genome evolution in the F. fujikuroi species complex.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Luca Degradi
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Valeria Tava
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Andrea Kunova
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Paolo Cortesi
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Marco Saracchi
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
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24
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Liu K, Xie N, Ma HJ. Next-generation sequencing reveals the mitogenomic heteroplasmy in the topmouth culter (Culter alburnus Basilewsky, 1855). Mol Biol Rep 2021; 49:943-950. [PMID: 34727288 DOI: 10.1007/s11033-021-06913-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND The mitogenomic heteroplasmy is the presence of multiple haplotypes in the mitochondria, which could cause genetic diseases and is also associated with many critical biological functions. The topmouth culter (Culter alburnus Basilewsky, 1855) is one of the most important freshwater fish in the family of Cyprinidae in China. At present, there are no reports on the topmouth culter's mtDNA heteroplasmy and the existence of which is not known. METHODS AND RESULTS This study aimed to analyze the mitogenomic heteroplasmy in the topmouth culter by the next-generation sequencing of the fins' total DNA. The results confirmed the existence of the heteroplasmy and indicated the presence of the extensive heteroplasmy in the topmouth culter's mitogenome. There were 38 heteroplasmic variations in the protein-coding genes from the three specimens, with 33 non-synonymous substitutions accounting for 86.84% and five synonymous substitutions accounting for 13.16%. Among them, the ND6 had the most heteroplasmic variations but only one synonymous substitution. After removing the putative nuclear mitochondrial DNA fragments, the ratio of primary haplotype in the three specimens was 43.89%, 74.72%, and 32.76%, respectively. The three specimens contained 21, 7, and 21 haplotypes of the mitogenomes, respectively. Due to the extensive heteroplasmy, we reconstructed the phylogenetic tree of the topmouth culter using the RY-coding method, which improved the performance of the phylogenetic tree to some extent. CONCLUSIONS This study reported the mitogenomic heteroplasmy in the topmouth culter and enhanced the knowledge regarding the mitogenomic heteroplasmy in phylogenetic studies. As the topmouth culter is a commercial species, the mitogenomic heteroplasmy is crucial for the fisheries management of the topmouth culter.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Heng-Jia Ma
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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25
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Yi M, Yang L, Zhou S. The complete chloroplast genome sequence of Prunus glandulosa Thunb. (Rosaceae). Mitochondrial DNA B Resour 2021; 6:3107-3108. [PMID: 34621990 PMCID: PMC8491658 DOI: 10.1080/23802359.2021.1982655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Prunus glandulosa Thunb. is an ornamental species in the genus Prunus (Rosaceae) mainly distributed in eastern China. It is often cultivated in gardens, roadsides, or shrub clusters. It looks like a cherry but resembles to prunes as well. We obtained the complete chloroplast genome of P. glandulosa using next-generation sequencing technology. The chloroplast genome is 158.078 bp in length with typical tetrad structure. It includes two copies of inverted repeats (IRs, 26.385 bp), a large single copy (LSC, 86.269 bp) and a small single copy (SSC, 19.039 bp). The total GC content is 36.7%, including 85 protein-coding genes (PCGs), 36 transfer RNA genes (tRNA), and eight ribosomal RNA genes (rRNA). The maximum-likelihood phylogeny using the full length of chloroplast genomes indicates that P. glandulosa is closer to prunes than to cherries.
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Affiliation(s)
- Meihong Yi
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Lixue Yang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, PR China
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26
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Liu K, Feng XY, Ma HJ, Xie N. Comparative mitochondrial genome analysis of the Mongolian redfin, Chanodichthys mongolicus (Xenocyprididae) from China reveals heteroplasmy. Mitochondrial DNA B Resour 2021; 6:2601-2604. [PMID: 34409154 PMCID: PMC8366642 DOI: 10.1080/23802359.2021.1961627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This study determined the mitochondrial genome (mitogenome) of Chanodichthys mongolicus from China's Qiantang River and analyzed its phylogenetic history in the Subfamily Cultrinae. Next-generation sequencing was used to obtain the mitogenome of C. mongolicus, GenBank Accession Number MZ032228. The mitochondrial genome length of C. mongolicus from China's Qiantang River is 16,622 bp. The genome contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two central noncoding regions (the control region and the origin of light strand replication). Based on BLAST comparisons, the sequence identity of C. mongolicus MZ032228 from China's Qiantang River was 99.84% to that of Ancherythroculter wangi MG783573 from China's Nei River, 99.75% to C. mongolicus AP009060 from Russia's Black River. The phylogenetic analysis is consistent with BLAST comparisons in confirming that A. wangi MG783573 and C. mongolicus MZ032228 show a high genetic similarity. This study also confirms mitochondrial DNA heteroplasmy in C. mongolicus for the first time and documents 35 heterogeneous loci that were detected.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xiao-yu Feng
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Heng-Jia Ma
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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27
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Ulaszewski B, Meger J, Mishra B, Thines M, Burczyk J. Complete Chloroplast Genomes of Fagus sylvatica L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs. Genes (Basel) 2021; 12:1357. [PMID: 34573338 PMCID: PMC8468245 DOI: 10.3390/genes12091357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 12/17/2022] Open
Abstract
Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of Fagus sylvatica, an important broadleaved tree species of European forests, based on complete chloroplast genomes of 18 individuals sampled widely across the species distribution. Our results confirm the hypothesis of a low cpDNA diversity in European beech. The chloroplast genome size was remarkably stable (158,428 ± 37 bp). The polymorphic markers, 12 microsatellites (SSR), four SNPs and one indel, were found only in the single copy regions, while inverted repeat regions were monomorphic both in terms of length and sequence, suggesting highly efficient suppression of mutation. The within-individual analysis of polymorphisms showed >9k of markers which were proportionally present in gene and non-gene areas. However, an investigation of the frequency of alternate alleles revealed that the source of this diversity originated likely from nuclear-encoded plastome remnants (NUPTs). Phylogeographic and Mantel correlation analysis based on the complete chloroplast genomes exhibited clustering of individuals according to geographic distance in the first distance class, suggesting that the novel markers and in particular the cpSSRs could provide a more detailed picture of beech population structure in Central Europe.
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Affiliation(s)
- Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
| | - Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
| | - Bagdevi Mishra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (B.M.); (M.T.)
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60483 Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (B.M.); (M.T.)
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60483 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany
| | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland; (J.M.); (J.B.)
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28
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Tian C, Li X, Wu Z, Li Z, Hou X, Li FY. Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae). Front Genet 2021; 12:705482. [PMID: 34422006 PMCID: PMC8378255 DOI: 10.3389/fgene.2021.705482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.
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Affiliation(s)
- Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiansong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Xiangyang Hou
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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29
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mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences. Life (Basel) 2021; 11:life11070633. [PMID: 34209862 PMCID: PMC8307225 DOI: 10.3390/life11070633] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects of heteroplasmy regarding its origin and its significance on mtDNA function and evolution, which has been progressively recognized in the last several years. Heteroplasmic organisms commonly occur through somatic mutations during an individual’s lifetime. They also occur due to leakage of paternal mtDNA, which rarely happens during fertilization. Alternatively, heteroplasmy can be potentially inherited maternally if an egg is already heteroplasmic. Recent advances in sequencing techniques have increased the ability to detect and quantify heteroplasmy and have revealed that mitochondrial DNA copies in the nucleus (NUMTs) can imitate true heteroplasmy. Heteroplasmy can have significant evolutionary consequences on the survival of mtDNA from the accumulation of deleterious mutations and for its coevolution with the nuclear genome. Particularly in humans, heteroplasmy plays an important role in the emergence of mitochondrial diseases and determines the success of the mitochondrial replacement therapy, a recent method that has been developed to cure mitochondrial diseases.
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30
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Chen R, Aldred MA, Xu W, Zein J, Bazeley P, Comhair SAA, Meyers DA, Bleecker ER, Liu C, Erzurum SC, Hu B. Comparison of whole genome sequencing and targeted sequencing for mitochondrial DNA. Mitochondrion 2021; 58:303-310. [PMID: 33513442 PMCID: PMC8354572 DOI: 10.1016/j.mito.2021.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
Mitochondrial dysfunction has emerged to be associated with a broad spectrum of diseases, and there is an increasing demand for accurate detection of mitochondrial DNA (mtDNA) variants. Whole genome sequencing (WGS) has been the dominant sequencing approach to identify genetic variants in recent decades, but most studies focus on variants on the nuclear genome. Whole genome sequencing is also costly and time consuming. Sequencing specifically targeted for mtDNA is commonly used in the diagnostic settings and has lower costs. However, there is a lack of pairwise comparisons between these two sequencing approaches for calling mtDNA variants on a population basis. In this study, we compared WGS and mtDNA-targeted sequencing (targeted-seq) in analyzing mitochondrial DNA from 1499 participants recruited into the Severe Asthma Research Program (SARP). Our study reveals that targeted-sequencing and WGS have comparable capacity to determine genotypes and to call haplogroups and homoplasmies on mtDNA. However, there exists a large variability in calling heteroplasmies, especially for low-frequency heteroplasmies, which indicates that investigators should be cautious about heteroplasmies acquired from different sequencing methods. Further research is highly desired to improve variant detection methods for mitochondrial DNA.
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Affiliation(s)
- Ruoying Chen
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Micheala A Aldred
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Weiling Xu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joe Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Suzy A A Comhair
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Chunyu Liu
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Serpil C Erzurum
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Bo Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
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31
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Godeiro NN, Bellini BC, Ding N, Xu C, Ding Y, Zhang F. A mitogenomic phylogeny of the Entomobryoidea (Collembola): A comparative perspective. ZOOL SCR 2021. [DOI: 10.1111/zsc.12487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nerivânia Nunes Godeiro
- Department of Entomology College of Plant Protection Nanjing Agricultural University Nanjing China
| | - Bruno Cavalcante Bellini
- Department of Botany and Zoology Biosciences Center Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil
| | - Nifeng Ding
- Department of Entomology College of Plant Protection Nanjing Agricultural University Nanjing China
| | - Cong Xu
- Department of Entomology College of Plant Protection Nanjing Agricultural University Nanjing China
| | - Yinhuan Ding
- Department of Entomology College of Plant Protection Nanjing Agricultural University Nanjing China
| | - Feng Zhang
- Department of Entomology College of Plant Protection Nanjing Agricultural University Nanjing China
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32
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Ricardo PC, Françoso E, Arias MC. Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification. Mitochondrion 2020; 53:243-254. [PMID: 32569843 DOI: 10.1016/j.mito.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/28/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Mitochondrial DNA (mtDNA) regions have been widely used as molecular markers in evolutionary studies and species identification. However, the presence of heteroplasmy and NUMTs may represent obstacles. Heteroplasmy is a state where an organism has different mitochondrial haplotypes. NUMTs are nuclear pseudogenes originating from mtDNA sequences transferred to nuclear DNA. Evidences of heteroplasmy were already verified in the bumblebee Bombus morio in an earlier study. The present work investigated in more detail the presence of intra-individual haplotypes variation in this species. Heteroplasmy was detected in individuals from all the ten sampled locations, with an average of six heteroplasmic haplotypes per individual. In addition, some of these heteroplasmic haplotypes were shared among individuals from different locations, suggesting the existence of stable heteroplasmy in B. morio. These results demonstrated that heteroplasmy is likely to affect inferences based on mtDNA analysis, especially in phylogenetic, phylogeographic and population genetics studies. In addition, NUMTs were also detected. These sequences showed divergence of 2.7% to 12% in relation to the mitochondrial haplotypes. These levels of divergence could mislead conclusions in evolutionary studies and affect species identification through DNA barcoding.
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Affiliation(s)
- Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Elaine Françoso
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
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